Comparative Assessment of Effectiveness of Alternative Genotyping Assays for Characterizing Carotenoids Accumulation in Tropical Maize Inbred Lines
The development of maize varieties with increased concentration of Provitamin A (PVA) is an effective and affordable strategy to combat vitamin A deficiency in developing nations. However, the considerably high cost of carotene analysis poses a major challenge for maize PVA biofortification, prompti...
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| Format: | Article |
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MDPI AG
2021-10-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/11/10/2022 |
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| author | Abdoul-Raouf Sayadi Maazou Melaku Gedil Victor O. Adetimirin Silvestro Meseka Wende Mengesha Deborah Babalola Queen Nkem Offornedo Abebe Menkir |
| author_facet | Abdoul-Raouf Sayadi Maazou Melaku Gedil Victor O. Adetimirin Silvestro Meseka Wende Mengesha Deborah Babalola Queen Nkem Offornedo Abebe Menkir |
| author_sort | Abdoul-Raouf Sayadi Maazou |
| collection | DOAJ |
| description | The development of maize varieties with increased concentration of Provitamin A (PVA) is an effective and affordable strategy to combat vitamin A deficiency in developing nations. However, the considerably high cost of carotene analysis poses a major challenge for maize PVA biofortification, prompting the use of marker-assisted selection. Presently, two types of genotyping with PVA trait-linked functional markers have been developed and extensively used in breeding programs. The two systems are low throughput gel-based genotyping and genotyping with Kompetitive Allele-Specific PCR (KASP) single nucleotide polymorphism (SNPs) markers. Although the KASP SNPs genotyping was developed to replace the gel-based genotyping, studies have not been conducted to compare the effectiveness of the KASP SNPs markers with the gel-based markers. This study was conducted to assess the carotenoid content of 64 tropical PVA biofortified maize inbred lines containing temperate germplasm in their genetic backgrounds and screen them with both gel-based and KASP markers of <i>PSY1</i>, <i>LCYE</i> and <i>crtRB1</i> genes. Many of the 64 inbred lines had PVA concentrations surpassing the 15 µg/g provitamin A breeding target set by the HarvestPlus Challenge Program. Favorable alleles of <i>crtRB1</i>, <i>crtRB1</i> and the KASP SNPs markers were detected in 25 inbred lines with high PVA concentrations. Inbred lines with the favorable alleles of <i>LCYE</i> had the highest concentrations of non-PVA carotenoids, whereas those with the favorable alleles of <i>crtRB1</i> had high levels of PVA carotenoids. Data from the sequenced region of <i>LCYE</i> revealed one SNP in the first intron that clearly differentiated the high and low β-carotene maize inbred lines. The results of our study demonstrate that the automated KASP SNPs markers can replace the gel-based genotyping for screening a large number of early generation maize inbred lines for PVA content. |
| first_indexed | 2024-03-10T06:47:39Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-10T06:47:39Z |
| publishDate | 2021-10-01 |
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| series | Agronomy |
| spelling | doaj.art-c88752527b054d89a656bc23b65659bf2023-11-22T17:07:03ZengMDPI AGAgronomy2073-43952021-10-011110202210.3390/agronomy11102022Comparative Assessment of Effectiveness of Alternative Genotyping Assays for Characterizing Carotenoids Accumulation in Tropical Maize Inbred LinesAbdoul-Raouf Sayadi Maazou0Melaku Gedil1Victor O. Adetimirin2Silvestro Meseka3Wende Mengesha4Deborah Babalola5Queen Nkem Offornedo6Abebe Menkir7Pan African University Life and Earth Sciences Institute (Including Health and Agriculture), University of Ibadan, Ibadan 200284, NigeriaInternational Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, NigeriaDepartment of Crop and Horticultural Sciences, University of Ibadan, PMB 5320, Ibadan 200284, NigeriaInternational Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, NigeriaInternational Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, NigeriaInternational Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, NigeriaInternational Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, NigeriaInternational Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, NigeriaThe development of maize varieties with increased concentration of Provitamin A (PVA) is an effective and affordable strategy to combat vitamin A deficiency in developing nations. However, the considerably high cost of carotene analysis poses a major challenge for maize PVA biofortification, prompting the use of marker-assisted selection. Presently, two types of genotyping with PVA trait-linked functional markers have been developed and extensively used in breeding programs. The two systems are low throughput gel-based genotyping and genotyping with Kompetitive Allele-Specific PCR (KASP) single nucleotide polymorphism (SNPs) markers. Although the KASP SNPs genotyping was developed to replace the gel-based genotyping, studies have not been conducted to compare the effectiveness of the KASP SNPs markers with the gel-based markers. This study was conducted to assess the carotenoid content of 64 tropical PVA biofortified maize inbred lines containing temperate germplasm in their genetic backgrounds and screen them with both gel-based and KASP markers of <i>PSY1</i>, <i>LCYE</i> and <i>crtRB1</i> genes. Many of the 64 inbred lines had PVA concentrations surpassing the 15 µg/g provitamin A breeding target set by the HarvestPlus Challenge Program. Favorable alleles of <i>crtRB1</i>, <i>crtRB1</i> and the KASP SNPs markers were detected in 25 inbred lines with high PVA concentrations. Inbred lines with the favorable alleles of <i>LCYE</i> had the highest concentrations of non-PVA carotenoids, whereas those with the favorable alleles of <i>crtRB1</i> had high levels of PVA carotenoids. Data from the sequenced region of <i>LCYE</i> revealed one SNP in the first intron that clearly differentiated the high and low β-carotene maize inbred lines. The results of our study demonstrate that the automated KASP SNPs markers can replace the gel-based genotyping for screening a large number of early generation maize inbred lines for PVA content.https://www.mdpi.com/2073-4395/11/10/2022provitamin Acarotenoidsbiofortificationmarker-assisted selectiontropical maize inbred lines |
| spellingShingle | Abdoul-Raouf Sayadi Maazou Melaku Gedil Victor O. Adetimirin Silvestro Meseka Wende Mengesha Deborah Babalola Queen Nkem Offornedo Abebe Menkir Comparative Assessment of Effectiveness of Alternative Genotyping Assays for Characterizing Carotenoids Accumulation in Tropical Maize Inbred Lines Agronomy provitamin A carotenoids biofortification marker-assisted selection tropical maize inbred lines |
| title | Comparative Assessment of Effectiveness of Alternative Genotyping Assays for Characterizing Carotenoids Accumulation in Tropical Maize Inbred Lines |
| title_full | Comparative Assessment of Effectiveness of Alternative Genotyping Assays for Characterizing Carotenoids Accumulation in Tropical Maize Inbred Lines |
| title_fullStr | Comparative Assessment of Effectiveness of Alternative Genotyping Assays for Characterizing Carotenoids Accumulation in Tropical Maize Inbred Lines |
| title_full_unstemmed | Comparative Assessment of Effectiveness of Alternative Genotyping Assays for Characterizing Carotenoids Accumulation in Tropical Maize Inbred Lines |
| title_short | Comparative Assessment of Effectiveness of Alternative Genotyping Assays for Characterizing Carotenoids Accumulation in Tropical Maize Inbred Lines |
| title_sort | comparative assessment of effectiveness of alternative genotyping assays for characterizing carotenoids accumulation in tropical maize inbred lines |
| topic | provitamin A carotenoids biofortification marker-assisted selection tropical maize inbred lines |
| url | https://www.mdpi.com/2073-4395/11/10/2022 |
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